Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4915N

Calculation Name: 3F1C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F1C

Chain ID: A

ChEMBL ID:

UniProt ID: Q720Y7

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2981456.754591
FMO2-HF: Nuclear repulsion 2888307.829907
FMO2-HF: Total energy -93148.924684
FMO2-MP2: Total energy -93420.756209


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-9.705-3.9472.591-3.696-4.652-0.017
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.025
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A2ILE0-0.002-0.0073.818-0.6291.030-0.018-0.705-0.9360.004
4A3TYR00.0240.0196.1560.7840.7840.0000.0000.0000.000
5A4ALA00.0040.0089.5670.0630.0630.0000.0000.0000.000
6A5GLN0-0.032-0.03512.8110.0080.0080.0000.0000.0000.000
7A6ILE0-0.0060.00215.7430.0350.0350.0000.0000.0000.000
8A7LEU00.0120.00917.8890.0240.0240.0000.0000.0000.000
9A8ALA0-0.030-0.02721.7160.0140.0140.0000.0000.0000.000
10A9GLY0-0.027-0.02125.4990.0010.0010.0000.0000.0000.000
11A10GLY00.0770.05124.204-0.001-0.0010.0000.0000.0000.000
12A11LYS10.9780.98125.2070.1100.1100.0000.0000.0000.000
13A12GLY00.0450.03328.7240.0000.0000.0000.0000.0000.000
14A13THR0-0.054-0.05732.2030.0040.0040.0000.0000.0000.000
15A14ARG10.9210.94335.7960.0730.0730.0000.0000.0000.000
16A15MET00.0560.05633.0110.0030.0030.0000.0000.0000.000
17A16GLY00.0490.01537.886-0.001-0.0010.0000.0000.0000.000
18A17ASN0-0.028-0.01933.033-0.002-0.0020.0000.0000.0000.000
19A18VAL00.0500.04335.556-0.002-0.0020.0000.0000.0000.000
20A19SER0-0.072-0.03835.9420.0020.0020.0000.0000.0000.000
21A20MET00.0050.02534.272-0.004-0.0040.0000.0000.0000.000
22A21PRO0-0.026-0.00429.6480.0000.0000.0000.0000.0000.000
23A22LYS10.9150.92731.4970.0940.0940.0000.0000.0000.000
24A23GLN00.0590.03326.5400.0100.0100.0000.0000.0000.000
25A24PHE0-0.0040.00028.637-0.003-0.0030.0000.0000.0000.000
26A25LEU0-0.0040.00531.7370.0070.0070.0000.0000.0000.000
27A26PRO0-0.010-0.00732.844-0.006-0.0060.0000.0000.0000.000
28A27LEU0-0.0160.00230.5270.0050.0050.0000.0000.0000.000
29A28ASN0-0.006-0.00933.3670.0000.0000.0000.0000.0000.000
30A29GLY00.0240.01235.085-0.001-0.0010.0000.0000.0000.000
31A30LYS10.8160.90727.8970.1310.1310.0000.0000.0000.000
32A31PRO00.0130.01229.876-0.001-0.0010.0000.0000.0000.000
33A32ILE0-0.0060.00427.812-0.007-0.0070.0000.0000.0000.000
34A33ILE00.029-0.00623.154-0.006-0.0060.0000.0000.0000.000
35A34VAL00.0040.01724.478-0.017-0.0170.0000.0000.0000.000
36A35HIS0-0.021-0.01624.666-0.014-0.0140.0000.0000.0000.000
37A36THR0-0.039-0.03521.210-0.002-0.0020.0000.0000.0000.000
38A37VAL00.0240.00720.003-0.021-0.0210.0000.0000.0000.000
39A38GLU-1-0.781-0.88119.673-0.174-0.1740.0000.0000.0000.000
40A39LYS10.8020.90719.5450.1680.1680.0000.0000.0000.000
41A40PHE00.004-0.00114.5250.0040.0040.0000.0000.0000.000
42A41ILE0-0.0010.01015.224-0.051-0.0510.0000.0000.0000.000
43A42LEU0-0.044-0.01616.8470.0000.0000.0000.0000.0000.000
44A43ASN0-0.055-0.02511.410-0.071-0.0710.0000.0000.0000.000
45A44THR00.014-0.00911.538-0.013-0.0130.0000.0000.0000.000
46A45ARG10.8130.8896.4520.2440.2440.0000.0000.0000.000
47A46PHE0-0.023-0.0027.408-0.401-0.4010.0000.0000.0000.000
48A47ASP-1-0.780-0.8906.490-2.195-2.1950.0000.0000.0000.000
49A48LYS10.8270.9179.7930.6370.6370.0000.0000.0000.000
50A49ILE0-0.040-0.02112.588-0.091-0.0910.0000.0000.0000.000
51A50LEU00.0090.00613.5260.0870.0870.0000.0000.0000.000
52A51ILE0-0.025-0.01316.9190.0040.0040.0000.0000.0000.000
53A52SER00.0120.01620.3620.0060.0060.0000.0000.0000.000
54A53SER0-0.037-0.03022.1070.0100.0100.0000.0000.0000.000
55A54PRO00.0260.02525.877-0.002-0.0020.0000.0000.0000.000
56A55LYS10.8950.92328.6650.1050.1050.0000.0000.0000.000
57A56GLU-1-0.865-0.94229.784-0.103-0.1030.0000.0000.0000.000
58A57TRP0-0.034-0.03430.3210.0050.0050.0000.0000.0000.000
59A58MET00.0060.02124.637-0.004-0.0040.0000.0000.0000.000
60A59ASN00.0430.01628.234-0.008-0.0080.0000.0000.0000.000
61A60HIS0-0.0030.00830.7210.0030.0030.0000.0000.0000.000
62A61ALA0-0.017-0.02026.396-0.001-0.0010.0000.0000.0000.000
63A62GLU-1-0.797-0.89124.135-0.181-0.1810.0000.0000.0000.000
64A63ASP-1-0.879-0.94127.125-0.100-0.1000.0000.0000.0000.000
65A64ASN0-0.076-0.05029.4500.0100.0100.0000.0000.0000.000
66A65ILE00.008-0.00323.2720.0030.0030.0000.0000.0000.000
67A66LYS10.9210.94523.9750.1510.1510.0000.0000.0000.000
68A67LYS10.8540.95127.1480.1070.1070.0000.0000.0000.000
69A68TYR0-0.074-0.04427.8920.0090.0090.0000.0000.0000.000
70A69ILE0-0.015-0.00521.891-0.001-0.0010.0000.0000.0000.000
71A70SER0-0.017-0.01024.4090.0000.0000.0000.0000.0000.000
72A71ASP-1-0.819-0.89117.582-0.320-0.3200.0000.0000.0000.000
73A72ASP-1-0.836-0.92916.796-0.274-0.2740.0000.0000.0000.000
74A73ARG10.7310.82512.7220.4990.4990.0000.0000.0000.000
75A74ILE0-0.0140.01116.168-0.052-0.0520.0000.0000.0000.000
76A75VAL00.0080.00416.6830.0320.0320.0000.0000.0000.000
77A76VAL0-0.0250.00219.457-0.027-0.0270.0000.0000.0000.000
78A77ILE0-0.027-0.01217.5050.0150.0150.0000.0000.0000.000
79A78GLU-1-0.798-0.90421.620-0.116-0.1160.0000.0000.0000.000
80A79GLY0-0.039-0.02822.612-0.017-0.0170.0000.0000.0000.000
81A80GLY0-0.011-0.01524.2140.0100.0100.0000.0000.0000.000
82A81GLU-1-0.929-0.96425.523-0.113-0.1130.0000.0000.0000.000
83A82ASP-1-0.802-0.88925.280-0.155-0.1550.0000.0000.0000.000
84A83ARG10.8290.90620.0900.2150.2150.0000.0000.0000.000
85A84ASN0-0.029-0.03420.838-0.040-0.0400.0000.0000.0000.000
86A85GLU-1-0.892-0.94220.450-0.159-0.1590.0000.0000.0000.000
87A86THR0-0.024-0.01820.706-0.006-0.0060.0000.0000.0000.000
88A87ILE00.0100.01515.676-0.021-0.0210.0000.0000.0000.000
89A88MET0-0.061-0.01216.596-0.037-0.0370.0000.0000.0000.000
90A89ASN0-0.020-0.00817.5750.0050.0050.0000.0000.0000.000
91A90GLY00.0070.01616.0080.0100.0100.0000.0000.0000.000
92A91ILE00.0130.00111.964-0.029-0.0290.0000.0000.0000.000
93A92ARG10.8950.93213.4890.2010.2010.0000.0000.0000.000
94A93PHE0-0.019-0.00415.1770.0360.0360.0000.0000.0000.000
95A94VAL00.0260.0199.3060.0470.0470.0000.0000.0000.000
96A95GLU-1-0.868-0.93411.888-0.089-0.0890.0000.0000.0000.000
97A96LYS10.8890.94712.8140.1630.1630.0000.0000.0000.000
98A97THR0-0.092-0.05214.7010.0490.0490.0000.0000.0000.000
99A98TYR0-0.039-0.03810.4530.0210.0210.0000.0000.0000.000
100A99GLY0-0.0080.03210.5540.1340.1340.0000.0000.0000.000
101A100LEU0-0.033-0.0197.883-0.088-0.0880.0000.0000.0000.000
102A101THR0-0.058-0.0393.641-0.1150.1540.001-0.062-0.2070.000
103A102ASP-1-0.903-0.9626.345-0.469-0.4690.0000.0000.0000.000
104A103ASP-1-0.873-0.9212.213-2.668-2.2511.930-1.187-1.160-0.006
105A104ASP-1-0.833-0.8932.862-6.184-3.4020.596-1.587-1.790-0.015
106A105ILE0-0.0040.0034.2490.9401.080-0.001-0.021-0.1190.000
107A106ILE0-0.024-0.0286.284-0.123-0.1230.0000.0000.0000.000
108A107VAL00.0080.0049.7130.1470.1470.0000.0000.0000.000
109A108THR0-0.056-0.03212.1640.0490.0490.0000.0000.0000.000
110A109HIS00.0880.01415.5700.0240.0240.0000.0000.0000.000
111A110ASP-1-0.804-0.89118.689-0.186-0.1860.0000.0000.0000.000
112A111ALA00.0740.01922.4850.0030.0030.0000.0000.0000.000
113A112VAL0-0.079-0.03623.9250.0080.0080.0000.0000.0000.000
114A113ARG10.8730.95323.0920.1800.1800.0000.0000.0000.000
115A114PRO00.0580.04223.618-0.015-0.0150.0000.0000.0000.000
116A115PHE0-0.064-0.04024.812-0.003-0.0030.0000.0000.0000.000
117A116LEU00.0500.04818.6030.0130.0130.0000.0000.0000.000
118A117THR00.025-0.00321.479-0.004-0.0040.0000.0000.0000.000
119A118HIS00.0640.01217.877-0.007-0.0070.0000.0000.0000.000
120A119ARG10.7380.85116.6520.0890.0890.0000.0000.0000.000
121A120ILE0-0.0190.00916.874-0.006-0.0060.0000.0000.0000.000
122A121ILE00.0180.00513.310-0.011-0.0110.0000.0000.0000.000
123A122GLU-1-0.792-0.87811.647-0.404-0.4040.0000.0000.0000.000
124A123GLU-1-0.813-0.90312.099-0.088-0.0880.0000.0000.0000.000
125A124ASN0-0.056-0.03412.9320.0030.0030.0000.0000.0000.000
126A125ILE0-0.005-0.0017.373-0.050-0.0500.0000.0000.0000.000
127A126ASP-1-0.833-0.9078.0860.1010.1010.0000.0000.0000.000
128A127ALA00.0060.0029.5970.0990.0990.0000.0000.0000.000
129A128ALA0-0.034-0.0198.4190.0190.0190.0000.0000.0000.000
130A129LEU0-0.010-0.0113.092-0.616-0.1250.083-0.134-0.4400.000
131A130GLU-1-0.870-0.8896.5220.1160.1160.0000.0000.0000.000
132A131THR0-0.018-0.0239.920-0.021-0.0210.0000.0000.0000.000
133A132GLY0-0.011-0.0019.471-0.029-0.0290.0000.0000.0000.000
134A133ALA00.001-0.01310.411-0.046-0.0460.0000.0000.0000.000
135A134VAL0-0.0280.00912.3250.0430.0430.0000.0000.0000.000
136A135ASP-1-0.772-0.88415.037-0.211-0.2110.0000.0000.0000.000
137A136THR0-0.018-0.00618.0060.0160.0160.0000.0000.0000.000
138A137VAL00.0260.01019.9540.0040.0040.0000.0000.0000.000
139A138ILE0-0.068-0.02123.5210.0020.0020.0000.0000.0000.000
140A139GLU-1-0.866-0.93026.699-0.056-0.0560.0000.0000.0000.000
141A140ALA0-0.027-0.01029.675-0.002-0.0020.0000.0000.0000.000
142A141LEU00.0190.00832.1840.0060.0060.0000.0000.0000.000
143A142ASP-1-0.950-0.98034.632-0.061-0.0610.0000.0000.0000.000
144A143THR0-0.045-0.03836.360-0.001-0.0010.0000.0000.0000.000
145A144ILE00.0280.02833.720-0.001-0.0010.0000.0000.0000.000
146A145VAL0-0.014-0.01137.2030.0030.0030.0000.0000.0000.000
147A146GLU-1-0.913-0.95135.825-0.057-0.0570.0000.0000.0000.000
148A147SER0-0.008-0.04039.4960.0030.0030.0000.0000.0000.000
149A148SER0-0.020-0.01140.921-0.002-0.0020.0000.0000.0000.000
150A149ASN0-0.011-0.01741.923-0.002-0.0020.0000.0000.0000.000
151A150HIS0-0.082-0.02940.125-0.001-0.0010.0000.0000.0000.000
152A151GLU-1-0.907-0.94044.726-0.038-0.0380.0000.0000.0000.000
153A152VAL0-0.038-0.02147.4590.0010.0010.0000.0000.0000.000
154A153ILE0-0.0150.00543.547-0.002-0.0020.0000.0000.0000.000
155A154THR0-0.063-0.04041.6570.0010.0010.0000.0000.0000.000
156A155ASP-1-0.835-0.92139.521-0.038-0.0380.0000.0000.0000.000
157A156ILE0-0.081-0.04040.254-0.002-0.0020.0000.0000.0000.000
158A157PRO00.0360.03735.8220.0020.0020.0000.0000.0000.000
159A158VAL0-0.011-0.00435.1890.0000.0000.0000.0000.0000.000
160A159ARG10.9010.93735.1150.0480.0480.0000.0000.0000.000
161A160ASP-1-0.872-0.92432.958-0.041-0.0410.0000.0000.0000.000
162A161HIS0-0.048-0.03730.777-0.002-0.0020.0000.0000.0000.000
163A162MET0-0.058-0.00829.957-0.007-0.0070.0000.0000.0000.000
164A163TYR00.0110.00626.536-0.001-0.0010.0000.0000.0000.000
165A164GLN0-0.051-0.02728.137-0.004-0.0040.0000.0000.0000.000
166A165GLY00.0590.03124.537-0.004-0.0040.0000.0000.0000.000
167A166GLN0-0.071-0.06322.896-0.003-0.0030.0000.0000.0000.000
168A167THR0-0.025-0.00319.597-0.002-0.0020.0000.0000.0000.000
169A168PRO0-0.013-0.02915.6860.0240.0240.0000.0000.0000.000
170A169GLN0-0.053-0.00316.3460.0240.0240.0000.0000.0000.000
171A170SER00.0040.00510.913-0.058-0.0580.0000.0000.0000.000
172A171PHE00.009-0.00310.9910.0830.0830.0000.0000.0000.000
173A172ASN00.0300.0126.704-0.067-0.0670.0000.0000.0000.000
174A173MET0-0.038-0.0107.5730.2960.2960.0000.0000.0000.000
175A174LYS10.8980.9379.1460.3910.3910.0000.0000.0000.000
176A175LYS10.8730.92711.0300.3300.3300.0000.0000.0000.000
177A176VAL00.0480.02812.7650.0690.0690.0000.0000.0000.000
178A177PHE0-0.034-0.02014.0950.0610.0610.0000.0000.0000.000
179A178ASN0-0.010-0.02314.6570.0500.0500.0000.0000.0000.000
180A179HIS0-0.025-0.02216.1660.0380.0380.0000.0000.0000.000
181A180TYR00.021-0.00218.6630.0250.0250.0000.0000.0000.000
182A181GLN0-0.014-0.02619.5280.0390.0390.0000.0000.0000.000
183A182ASN00.0000.00820.6180.0230.0230.0000.0000.0000.000
184A183LEU0-0.0520.00023.0190.0150.0150.0000.0000.0000.000
185A184THR0-0.015-0.01525.6930.0030.0030.0000.0000.0000.000
186A185PRO00.044-0.00228.780-0.005-0.0050.0000.0000.0000.000
187A186GLU-1-0.810-0.91130.266-0.082-0.0820.0000.0000.0000.000
188A187LYS10.9070.95827.8870.0760.0760.0000.0000.0000.000
189A188LYS10.8670.95524.0700.1210.1210.0000.0000.0000.000
190A189GLN0-0.0440.00027.197-0.010-0.0100.0000.0000.0000.000
191A190ILE0-0.072-0.03830.0980.0010.0010.0000.0000.0000.000
192A191LEU0-0.069-0.03625.0470.0020.0020.0000.0000.0000.000
193A192THR00.0350.01525.229-0.011-0.0110.0000.0000.0000.000
194A193ASP-1-0.825-0.89822.475-0.190-0.1900.0000.0000.0000.000
195A194ALA00.0660.02218.0810.0070.0070.0000.0000.0000.000
196A195CYS0-0.010-0.01418.266-0.021-0.0210.0000.0000.0000.000
197A196LYS10.9510.98219.5140.1130.1130.0000.0000.0000.000
198A197ILE0-0.033-0.01619.8870.0130.0130.0000.0000.0000.000
199A198CYS0-0.023-0.00516.653-0.004-0.0040.0000.0000.0000.000
200A199LEU00.0230.02618.8190.0120.0120.0000.0000.0000.000
201A200LEU0-0.088-0.05621.5270.0140.0140.0000.0000.0000.000
202A201ALA0-0.048-0.01319.7760.0110.0110.0000.0000.0000.000
203A202GLY0-0.030-0.01120.8450.0030.0030.0000.0000.0000.000
204A203ASP-1-0.819-0.88315.298-0.205-0.2050.0000.0000.0000.000
205A204ASP-1-0.902-0.94416.798-0.058-0.0580.0000.0000.0000.000
206A205VAL0-0.063-0.03015.987-0.022-0.0220.0000.0000.0000.000
207A206LYS10.8230.89614.7390.0220.0220.0000.0000.0000.000
208A207LEU00.0180.00117.243-0.023-0.0230.0000.0000.0000.000
209A208VAL00.0040.01615.5130.0160.0160.0000.0000.0000.000
210A209LYS10.9170.96118.7780.0810.0810.0000.0000.0000.000
211A210GLY00.0500.00821.617-0.010-0.0100.0000.0000.0000.000
212A211GLU-1-0.867-0.92923.191-0.084-0.0840.0000.0000.0000.000
213A212ILE00.0640.03626.373-0.006-0.0060.0000.0000.0000.000
214A213PHE00.0320.00525.994-0.001-0.0010.0000.0000.0000.000
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